Prof Reiss's views were known to the Royal Society when it appointed him. Photograph: Frank Baron

Britain's national academy of science parted company with its director of education yesterday following a furore over the teaching of creationism in schools.

Michael Reiss, a professor of education at the Institute of Education in London and an ordained Church of England clergyman, agreed to step down from his position at the Royal Society, which claimed that he had unintentionally caused damage to the organisation's reputation.

The Royal Society announced Reiss's resignation in a statement today. It said: "Some of Professor Michael Reiss's recent comments, on the issue of creationism in schools, while speaking as the Royal Society's Director of Education, were open to misinterpretation. While it was not his intention, this has led to damage to the Society's reputation. As a result, Professor Reiss and the Royal Society have agreed that, in the best interests of the Society, he will step down immediately as director of education." In his speech, Reiss said that while creationism had no scientific basis, science teachers risked alienating pupils who believed in the idea by dismissing it out of hand. "They should take the time to explain how science works and why creationism has no scientific basis," he said.

Reiss's resignation met with a mixed response yesterday. The fertility specialist Lord Winston commented: "I fear that in this action the Royal Society may have only diminished itself. This is not a good day for the reputation of science or scientists. This individual was arguing that we should engage with and address public misconceptions about science – something that the Royal Society should applaud."

But Phil Willis, chairman of the Commons Innovation, Universities, Science and Skills Committee, said: "It's the right decision and it's clearly one the Royal Society needed to come to itself. You cannot have a senior educational figure in the world's most prestigious scientific society giving credence to creationism alongside Darwinism in the school curriculum. By allowing creationism to have a part in the science curriculum alongside Darwinism, it gives them equal merit."

Reiss will now return to a full-time job at the Institute of Education, University of London. Dylan Wiliam deputy director of the institute, said: "The Royal Society appears to be taking a precautionary approach and distancing themselves from what people might make of his comments rather than what he actually said.

"Michael is a very important figure in science education, and a world respected academic for his ability to analyse difficult moral issues. He's a science educator and scientist by training but also a reverend, and he doesn't see these things as incompatible. I have great respect for his views."

The Royal Society would already have been aware of Reiss's opinions about discussing creationism in science classes. In a book published last year called Teaching about Scientific Origins: Taking Account of Creationism, Reiss said teachers should expect to encounter more children with creationist views and urged them to be prepared to discuss the issue.

Barry Sheerman, chair of the Commons education committee, said he was saddened at Reiss's resignation and felt he had been treated harshly by the Royal Society.

"My view has always been that while creationism shouldn't be part of the science curriculum, there's nothing wrong with it being on the curriculum in some shape or form, because it opens up a debate that is more philosophical. It seems to me that Michael Reiss said what he did with the best intentions, that science teachers should engage with pupils who have creationist views, and I agreed with that," said Sheerman.

"The Royal Society is a wonderful institution with wonderful people, but this has got out of hand. It's an over-reaction, and I wish the people at the Society would sit down and think about this and act in a more grown-up fashion. This sort of nonsense doesn't do anyone any good."